I was using RH 6.0, on /dev/sda5, with LILO installed on
/dev/sda5 (and /etc/lilo.conf also knew that). I use System
Commander on my MBR and winndows on /dev/sda1. When I
upgraded to 6.1, by booting from the CD-ROM and choosing the
custom upgrade option, the RH setup program installed LILO
on my MBR!!!
	As a result, I couldn't boot my windows partition
(/dev/sda1) but Linux booted ok. I had to reinstall System
Commander. Then I couldn't boot Linux!!! Maybe because the
kernel changed, lilo (the one on /dev/sda5) stopped after
saying 'LIL-'.
	I spent 2 days trying to install lilo again, from a boot
disk, because it complained about 'First boot sector does
not contain a valid boot sector' whether I tried it on
/dev/sda or /dev/sda5. The other day, when I was trying to
install it for the last time, before tragically formatting
my Linux partition, it installed (with no special options
whatsoever).
	Well, sorry if I wrote too much, but I really got pissed at
the RH setup stuff. It REALLY should read /etc/lilo.conf or
something to know where lilo is.